CYANA Command: structures secondary: Difference between revisions
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; structures=''integer'': (default: 1) | ; structures=''integer'': (default: 1) | ||
; mode=classic|normal|psipred|simple|ovw|sep: (default: normal) | ; mode=classic|normal|psipred|simple|ovw|sep: (default: normal) | ||
== Description == | |||
Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to '''full''' or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of ''structures'', as defined by the '''structures''' parameter. The default is to use all hydrogen bonds that are found in any structure. | Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to '''full''' or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of ''structures'', as defined by the '''structures''' parameter. The default is to use all hydrogen bonds that are found in any structure. | ||
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The following '''mode'''s are supported for the output of the results: | The following '''mode'''s are supported for the output of the results: | ||
; classic: Output exactly as in the DSSP publication (Kabsch & Sander, 1983) | |||
; normal: Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters. | |||
; psipred: Single-line output in the format of the program [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred]. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'. | |||
;; | ;simple: Output only information on helices and β-strands. In the summary line, these are designated '3' for 3<sub>10</sub>-helices, 'H' for α-helices, and 'B' for β-strands. | ||
; ovw: List the secondary structure elements, one per line. | |||
; seo: Similar output of the secondary structure elements one per line, separate for helices and β-sheets. | |||
Latest revision as of 14:53, 31 July 2011
Parameters
- structures=integer
- (default: 1)
- mode=classic|normal|psipred|simple|ovw|sep
- (default: normal)
Description
Computes the secondary structure using the DSSP algorithm (Kabsch & Sander, 1983), which is based exclusively on the detection of hydrogen bonds. If multiple structures are selected, the secondary structure is reported for the individual structures only if information level is set to full or higher. Otherwise only the consensus secondary structure is reported. The consensus secondary structure for a structure bundle is obtained by considering all hydrogen bonds that occur in a minimal number of structures, as defined by the structures parameter. The default is to use all hydrogen bonds that are found in any structure.
The following modes are supported for the output of the results:
- classic
- Output exactly as in the DSSP publication (Kabsch & Sander, 1983)
- normal
- Same as 'classic', except that in the summary line bends ('s') and turns ('t') are indicated with lower instead of upper case letters.
- psipred
- Single-line output in the format of the program PsiPred. Helices are indicated by 'H', β-strands by 'E', and all other residues are designated 'C'.
- simple
- Output only information on helices and β-strands. In the summary line, these are designated '3' for 310-helices, 'H' for α-helices, and 'B' for β-strands.
- ovw
- List the secondary structure elements, one per line.
- seo
- Similar output of the secondary structure elements one per line, separate for helices and β-sheets.